Change strict restriction on PointFinder organisms to be a warning about staramr HOT 2 CLOSED

Hi @apetkau,
Thanks to yours comments, I take time to answer to learn python and oriented object programming to understand your work !
My first conclusion was the same as you.

• Instead of using the get_available_organisms(cls) method maybe the get_organisms(cls, database_dir) already existing do the job ! It use the information from the config file into pointfinder directory and you already created a test to check diff between organism
  I'm just trying to understand how to refer to the new method
• Then for pointfinder nucleotide analysis, I will try to translate all nucleotide position into positive value (as you mentioned for promoter region with negative position) to be use in your code. I think some changes in the CodonMutationPosition.py to be more flexible ?

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Hello @pimarin,

That's awesome you've taken the time to learn Python and Object Oriented programming 😄. I hope it is going well for you. I can be a very useful language to learn. Another important library I use throughout staramr is pandas for manipulation of data in Python (in particular, loading and working with CSV files or other tabular data structures). And then, while I don't use these in staramr, this could lead into learning about matplotlib or seaborn for creating visual plots of data. But this is all quite a bit to learn (and is a bit outside of what staramr handles).

1. Yes, the get_organisms() method is used to load up all the PointFinder organism name available in the currently-installed version of the PointFinder database:

   staramr/staramr/blast/pointfinder/PointfinderBlastDatabase.py

   Lines 86 to 94 in fd4c230

   	def get_organisms(cls, database_dir):
   	"""
   	A Class Method to get the list of organisms from the PointFinder database root directory.
   	:param database_dir: The PointFinder database root directory.
   	:return: A list of organisms.
   	"""
   	config = pd.read_csv(path.join(database_dir, 'config'), sep='\t', comment='#', header=None,
   	names=['db_prefix', 'name', 'description'])
   	return config['db_prefix'].tolist()

   Just to clarify, the reason I use get_available_organisms() instead of get_organisms() to return a list of organisms to use for PointFinder is because anything not returned by get_available_organisms() is not guaranteed to work in staramr. That is it was a decision I made to prevent staramr from returning potentially invalid results. This particular issue would be a compromise where instead of disallowing people from running staramr with organisms not returned by get_available_organisms(), I would simply print a warning.

2. Thanks so much for offering to help out with looking into supporting those other coordinates for PointFinder databases (negative coordinates or insertions/deletions). I really do appreciate it. I would welcome any contributions you can make.

   However, note that I have someone in my group who will be looking into this issue too. I want to be a bit more open about my plans for staramr, so I have started to write up my plans in the Projects section of GitHub. There are two projects you can see here:

   1. Release 0.8.0: This will update the default databases for staramr and I will try to include fixing this issue (where you can run staramr with other PointFinder organisms, but you will get a warning printed).
   2. Release 1.0.0: This will include full support for other PointFinder organisms by supporting insertions/deletions/promotor regions leading to AMR.

   I hope this all makes sense? Again, I would welcome any suggestions or contributions you may have. But we do plan to work on fixing up some of these issues and packaging them up into new staramr releases.

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